* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/disprose.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘disprose/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘disprose’ version ‘0.1.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘disprose’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/disprose-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [10s/12s] OK
* checking Rd files ... [1s/1s] NOTE
checkRd: (-1) store_in_DB.Rd:89: Lost braces
    89 | link{read_from_DB} function. Those parameters define rows and columns that will be returned.
       |     ^
checkRd: (-1) unite_two_DF.Rd:46: Lost braces; missing escapes or markup?
    46 | \code{data1.shared.var} and {data2.shared.var} must contain unique values within its own data frame.
       |                             ^
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [1s/22s] ERROR
Running examples in ‘disprose-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cut_probes
> ### Title: Cut probes
> ### Aliases: cut_probes
> 
> ### ** Examples
> 
> path <- tempdir()
> dir.create (path)
> # download and save as FASTA "Chlamydia pneumoniae B21 contig00001,
> # whole genome shotgun sequence" (GI = 737435910)
> if (!requireNamespace("rentrez", quietly = TRUE)) {
+ stop("Package \"rentrez\" needed for this function to work. Please install it.", call. = FALSE)}
> reference.string <- rentrez::entrez_fetch(db = "nucleotide", id = 737435910,
+                                          rettype="fasta")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [eutils.ncbi.nlm.nih.gov]: Resolving timed out after 10000 milliseconds
Calls: <Anonymous> ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
* checking PDF version of manual ... [5s/8s] OK
* checking HTML version of manual ... [2s/3s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE